INOSINE ADENOSINE BASE-PAIRING IN D-GGTACIAGTACC - DUPLEX AND HAIRPINWITH A 2-BASE LOOP

An oligonucleotide dodecamer d-GGTACIAGTACC containing two inosine-ade nosine mismatched base-pairs has been studied by H-1 and P-31 NMR spec troscopy. Unique assignments of H-1 and P-31 spins have been achieved by using a recently proposed two-dimensional heteronuclear long range correlation (2D-HELCO) technique. The 2D nuclear Overhauser enhancemen t spectroscopy (NOESY) spectrum recorded in a mixed solvent of 90% H2O + 10% (H2O)-H-2 has been used to assign all the exchangeable imino an d amino proton resonances. NMR results indicate that at concentrations above 5 mM, the molecule adopts a duplex structure where the inosine imino protons are hydrogen bonded. Cross-strand NOEs between the imino proton of I6 and H2 proton of A7 and that between H2 of I6 and H2 of A7 provide evidence for inosine-adenosine base-pairing, with both base s I6 and A7 in anti conformation. The observed NOE connectivities d1, d2 and d3 from almost the middle of the molecule to the two ends are c onsistent with a right handed B-DNA conformation. However, the molecul e adopts a more extended conformation in the mismatch region to accomm odate the bulky purine-purine (IA) base pairs. NMR experiments at lowe r concentrations indicate the coexistence of a monomeric hairpin with a two base loop, consisting of I6 and A7 units, in equilibrium with th e duplex. 2D-ROESY experiment at such a concentration shows that the c onformation of the stem of the hairpin does not deviate much from the corresponding region of the duplex and four nucleotides C5, I6, A7 and G8 undergo significant structural changes during the formation of hai rpin loop.